SMTL ID : 1zn7.1

Human Adenine Phosphoribosyltransferase Complexed with PRPP, ADE and R5P

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.83 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: D.65, S.66, D.127 Ligands: PO4.2, PRP.4, HSX.5 No protein-ligand interaction detected (PLIP) MG.7: 6 residues within 4Å: Chain B: D.65, S.66, D.127 Ligands: PO4.3, PRP.8, HSX.9 No protein-ligand interaction detected (PLIP)

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 8 residues within 4Å: Chain A: D.65, S.66, R.67 Chain B: R.87, K.91 Ligands: MG.1, PRP.4, HSX.5 9 PLIP interactions: 2 interactions with chain B, 7 interactions with chain A Salt bridges: B:R.87, B:K.91, A:R.67, A:K.88 Hydrogen bonds: A:S.66, A:R.67 Water bridges: A:G.68, A:K.88, A:K.88 PO4.3: 8 residues within 4Å: Chain A: R.87, K.91 Chain B: D.65, S.66, R.67 Ligands: MG.7, PRP.8, HSX.9 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.66, B:R.67 Salt bridges: B:R.67, A:R.87, A:K.91 Water bridges: A:R.87

2 x PRP: 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose(Non-covalent)

PRP.4: 19 residues within 4Å: Chain A: D.65, S.66, R.67, K.88, L.103, D.127, D.128, L.129, A.131, T.132, G.133, G.134, T.135 Chain B: R.87, K.91 Ligands: MG.1, PO4.2, HSX.5, ADE.6 27 PLIP interactions: 24 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:S.66, A:R.67, A:D.127, A:A.131, A:T.132, A:G.133, A:G.134, A:T.135, A:T.135 Water bridges: A:S.66, A:R.67, A:K.88, A:K.88, A:K.88, A:K.88, A:D.127, A:T.132, A:T.132, A:M.136 Salt bridges: A:R.67, A:R.67, A:R.67, A:K.88, A:K.88, B:R.87, B:K.91, B:K.91 PRP.8: 18 residues within 4Å: Chain A: R.87, K.91 Chain B: D.65, S.66, R.67, L.103, D.127, D.128, L.129, A.131, T.132, G.133, G.134, T.135 Ligands: PO4.3, MG.7, HSX.9, ADE.10 21 PLIP interactions: 16 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:S.66, B:R.67, B:D.127, B:A.131, B:T.132, B:G.133, B:G.134, B:T.135, B:T.135 Water bridges: B:R.67, B:T.132, B:T.132, B:M.136, A:R.87 Salt bridges: B:R.67, B:R.67, B:R.67, A:R.87, A:K.91, A:K.91, A:K.91

2 x HSX: 5-O-phosphono-alpha-D-ribofuranose(Non-covalent)

HSX.5: 14 residues within 4Å: Chain A: R.67, D.127, D.128, L.129, L.130, A.131, T.132, G.133, G.134, T.135 Ligands: MG.1, PO4.2, PRP.4, ADE.6 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:D.127, A:A.131, A:T.132, A:G.133, A:G.134, A:T.135 Water bridges: A:S.66, A:R.67, A:R.67, A:T.132, A:T.132, A:M.136 Salt bridges: A:R.67 HSX.9: 14 residues within 4Å: Chain B: R.67, D.127, D.128, L.129, L.130, A.131, T.132, G.133, G.134, T.135 Ligands: PO4.3, MG.7, PRP.8, ADE.10 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:D.127, B:A.131, B:T.132, B:G.133, B:G.134, B:T.135, B:T.135 Water bridges: B:S.66, B:S.66, B:R.67, B:R.67, B:T.132, B:T.132, B:T.135, B:M.136 Salt bridges: B:R.67

2 x ADE: ADENINE(Non-covalent)

ADE.6: 9 residues within 4Å: Chain A: V.25, F.26, R.27, R.67, L.129, A.131, L.159 Ligands: PRP.4, HSX.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.27, A:R.67, A:R.67 ADE.10: 9 residues within 4Å: Chain B: V.25, F.26, R.27, R.67, L.129, A.131, L.159 Ligands: PRP.8, HSX.9 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.27, B:R.67, B:R.67

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Silva, C.H. et al., Structural Complexes of Human Adenine Phosphoribosyltransferase Reveal Novel Features of the APRT Catalytic Mechanism. J.Biomol.Struct.Dyn. (2008)

Release Date

2006-04-25

Peptides

Adenine phosphoribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Adenine phosphoribosyltransferase

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